Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 973,213 C→A 100% E175* (GAG→TAG)  yitU_1 ← 5‑amino‑6‑(5‑phospho‑D‑ribitylamino)uracil phosphatase YitU

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE973,2130CA100.0% 93.0 / NA 30E175* (GAG→TAG) yitU_15‑amino‑6‑(5‑phospho‑D‑ribitylamino)uracil phosphatase YitU
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base A (18/12);  total (18/12)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TCTTCATCACCGAATGCAATAATATTATTTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTCAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGACAAGTAAATTACCAGTTTGAATTCTTGGATTAC  >  USA300TCH1516_ALE/973077‑973347
                                                                                                                                        |                                                                                                                                      
tCTTCATGACCGAATGCAATATTATTATTTCGGTAAATCTTTAGAAATTGTCTAGCTAGCTCAATGCATCTTTCTTTATTAATACCAAGTTTTACCATTTCGCTGACAGGGCGTGTTGCACCCCAGAGTCGCTGCTAAata                                                                                                                                    >  2:300124/1‑141 (MQ=255)
         ccGAATGCAATAATATTATTTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCa                                                                                                                           >  1:351300/1‑141 (MQ=255)
               tcAATAATATTTTTTCGGTCAATATTTAAAAAGTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCTGCGTCGATGCTAAATATGATCGGCATaaaaa                                                                                                                     <  2:117013/140‑1 (MQ=255)
               gCAATAATATTATTTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATaatta                                                                                                                     >  2:398402/1‑138 (MQ=255)
                   taataTTATTTCGGTCAATATTTAAAAATTGTCTAACTTGCTCTATTCCGCTTTCTTTATTCATACGAAGTTTTACATTTTCAATGACAGGGAATGGTGCGCCCCAGCGGCGATGCTAAATATGATCGGCATAAAAATGAg                                                                                                                 <  2:141983/141‑1 (MQ=255)
                       attattTCGGTCAATATTTACAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAg                                                                                                             <  2:301721/141‑1 (MQ=255)
                       attattTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAg                                                                                                             <  2:172427/141‑1 (MQ=255)
                       attattTCGGTCAATATTTAAAAATTGTCTAACTTACTCAATGCCACTTTCCTTAATAATACCAACGGTTACAATTTCAATGACATTGAATGTTGCGCCCCAGCTTCGATGCTAAATATGATCGGCATAAAAATGAGTAAg                                                                                                             <  2:231144/141‑1 (MQ=255)
                         tattTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCa                                                                                                           <  1:134423/141‑1 (MQ=255)
                         tattTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGACTCTTGCTCTATTAATACCTAGTTGTACAATTTCCATGCATGGTGAGGACCCGCCCCAGCGGCGATACGAAATATGATCGGCATAAAAAGGAGTAAGCa                                                                                                           >  2:382855/1‑141 (MQ=255)
                           tttCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCata                                                                                                         >  1:229734/1‑141 (MQ=255)
                                  cAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATAtttttaa                                                                                                  >  2:39579/1‑139 (MQ=255)
                                   aaTATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCTTCGATGCTAAATATGATCGGCATAAAAATCAGTAAGCATATTTTTGAt                                                                                                 >  2:73645/1‑141 (MQ=255)
                                   aaTATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGAt                                                                                                 <  1:178583/141‑1 (MQ=255)
                                        ttcaataTTGTCTTACTTGCTCAATGCCTCTGGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAg                                                                                            <  2:80996/135‑1 (MQ=255)
                                                tGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATCTGACCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTa                                                                                    <  1:77589/141‑1 (MQ=255)
                                                tGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTAAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTa                                                                                    >  1:133114/1‑141 (MQ=255)
                                                     aaCTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTttc                                                                               >  1:21851/1‑141 (MQ=255)
                                                      aCTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTttct                                                                              >  2:116694/1‑141 (MQ=255)
                                                      aCTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTttct                                                                              >  2:173015/1‑141 (MQ=255)
                                                           cTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAAAGCGTGAGATTTTTTTTGATTTCAGGTATTTTACTTTCTTCGGc                                                                         >  1:372039/1‑141 (MQ=255)
                                                                 gCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAAt                                                                   <  2:68206/141‑1 (MQ=255)
                                                                        gCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAAtt                                                            >  1:330508/1‑141 (MQ=255)
                                                                          tttATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCCTAAAAATGAGTATGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGTCTTCCATTTATATTgg                                                          >  2:39334/1‑140 (MQ=255)
                                                                                 aTACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTGCAATTAAAATTGAGGTAggt                                                   <  2:134820/141‑2 (MQ=255)
                                                                                        gTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCtt                                            <  1:375549/141‑1 (MQ=255)
                                                                                         ttttACAATTTCAATGACAGGGAATGGTGCGCCCCAGAGTCGGTGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTTTTCGGCTTCAATTAAAGTTGAGGAGGGGGTTTCttt                                           >  1:112880/1‑141 (MQ=255)
                                                                                             aCAATTTCAATGACAGAGAATGGTGCGCCCCAGCGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAg                                       >  1:198038/1‑141 (MQ=255)
                                                                                                         aCAGGGAATGGTGCGCCCCAACGTCGATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGACAAGTaaa                           >  1:319928/1‑141 (MQ=255)
                                                                                                                                  gATGCTAAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGACAAGTAAATTACCAGTTTGAATTCTTGGATTAc  >  1:36863/1‑141 (MQ=255)
                                                                                                                                        |                                                                                                                                      
TCTTCATCACCGAATGCAATAATATTATTTCGGTCAATATTTAAAAATTGTCTAACTTGCTCAATGCCTCTTGCTTTATTAATACCAAGTTTTACAATTTCAATGACAGGGAATGGTGCGCCCCAGCGTCGATGCTCAATATGATCGGCATAAAAATGAGTAAGCATATTTTTGATTTCAGGTATTTTACTTTCTTCGGCTTCAATTAAAATTGAGGTAGGGGATTCTTTCAAGTGGACAAGTAAATTACCAGTTTGAATTCTTGGATTAC  >  USA300TCH1516_ALE/973077‑973347

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑